A population model for genotyping indels from next-generation sequence data.
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ABSTRACT:
SUBMITTER: Shao H
PROVIDER: S-EPMC3562001 | biostudies-literature | 2013 Feb
REPOSITORIES: biostudies-literature
Publications
A population model for genotyping indels from next-generation sequence data.
Shao Haojing H Bellos Evangelos E Yin Hanjiudai H Liu Xiao X Zou Jing J Li Yingrui Y Wang Jun J Wang Jun J Coin Lachlan J M LJ
Nucleic acids research 20121205 3
Insertion and deletion polymorphisms (indels) are an important source of genomic variation in plant and animal genomes, but accurate genotyping from low-coverage and exome next-generation sequence data remains challenging. We introduce an efficient population clustering algorithm for diploids and polyploids which was tested on a dataset of 2000 exomes. Compared with existing methods, we report a 4-fold reduction in overall indel genotype error rates with a 9-fold reduction in low coverage region ...[more]
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